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Special Issue "Modern Analytical Techniques in Metabolomics Analysis"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Analytical Chemistry".

Deadline for manuscript submissions: closed (31 July 2020).

Special Issue Editor

Prof. Dr. Jesus Simal-Gandara
grade E-Mail Website
Guest Editor
Department of Analytical Chemistry and Food Science, Faculty of Food Science and Technology, University of Vigo, Ourense Campus, E-32004 Ourense, Spain
Interests: phenolic compounds; antioxidants; marine drugs; food safety; bioaccessibility; functional foods
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Metabolomics is the complete evaluation of endogenous metabolites and aims to systematically identify and quantify metabolites from a biological sample. Small molecule metabolites play an important role in biological systems and are interesting candidates for understanding the phenotypes of an organism. The metabolites represent a heterogeneous group of low molecular weight structures, including lipids, amino acids, peptides, nucleic acids, organic acids, vitamins, thiols and carbohydrates, making the overall analysis difficult. The recent rapid development of a range of analysis platforms, including GC, UPLC, CE, etc., coupled with MS and NMR spectroscopy, could allow the separation, detection, characterization and quantification of these metabolites and associated metabolic pathways. The combined use of modern instrumental analytical approaches is useful for increasing the coverage of the detected metabolites that cannot be achieved with single analytical techniques. The continuous development of these analytical platforms will accelerate the widespread use and integration of metabolomics in systems biology. This section will highlight the role of integrated tools in metabolomics research.

Prof. Dr. Jesus Simal-Gandara
Guest Editor

Manuscript Submission Information

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Keywords

  • metabolomics
  • untargeted methods
  • targeted methods
  • analytical chemistry
  • biomarkers
  • profiling
  • fingerprinting

Published Papers (11 papers)

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Research

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Article
Biochemical and Computational Approach of Selected Phytocompounds from Tinospora crispa in the Management of COVID-19
Molecules 2020, 25(17), 3936; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25173936 - 28 Aug 2020
Cited by 29 | Viewed by 3289
Abstract
A pandemic caused by the novel coronavirus (SARS-CoV-2 or COVID-19) began in December 2019 in Wuhan, China, and the number of newly reported cases continues to increase. More than 19.7 million cases have been reported globally and about 728,000 have died as of [...] Read more.
A pandemic caused by the novel coronavirus (SARS-CoV-2 or COVID-19) began in December 2019 in Wuhan, China, and the number of newly reported cases continues to increase. More than 19.7 million cases have been reported globally and about 728,000 have died as of this writing (10 August 2020). Recently, it has been confirmed that the SARS-CoV-2 main protease (Mpro) enzyme is responsible not only for viral reproduction but also impedes host immune responses. The Mpro provides a highly favorable pharmacological target for the discovery and design of inhibitors. Currently, no specific therapies are available, and investigations into the treatment of COVID-19 are lacking. Therefore, herein, we analyzed the bioactive phytocompounds isolated by gas chromatography–mass spectroscopy (GC-MS) from Tinospora crispa as potential COVID-19 Mpro inhibitors, using molecular docking study. Our analyses unveiled that the top nine hits might serve as potential anti-SARS-CoV-2 lead molecules, with three of them exerting biological activity and warranting further optimization and drug development to combat COVID-19. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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Article
Workflow for the Quantification of Soluble and Insoluble Carbohydrates in Soybean Seed
Molecules 2020, 25(17), 3806; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25173806 - 21 Aug 2020
Cited by 1 | Viewed by 1258
Abstract
Soybean seed composition has a profound impact on its market value and commercial use as an important commodity. Increases in oil and protein content have been historically pursued by breeders and genetic engineers; consequently, rapid methods for their quantification are well established. The [...] Read more.
Soybean seed composition has a profound impact on its market value and commercial use as an important commodity. Increases in oil and protein content have been historically pursued by breeders and genetic engineers; consequently, rapid methods for their quantification are well established. The interest in complete carbohydrate profiles in mature seeds, on the other hand, has recently increased due to numerous attempts to redirect carbohydrates into oil and protein or to offer specialty seed with a specific sugar profile to meet animal nutritional requirements. In this work, a sequential protocol for quantifying reserve and structural carbohydrates in soybean seed was developed and validated. Through this procedure, the concentrations of soluble sugars, sugar alcohols, starch, hemicellulose, and crystalline cellulose can be determined in successive steps from the same starting material using colorimetric assays, LC–MS/MS, and GC–MS. The entire workflow was evaluated using internal standards to estimate the recovery efficiency. Finally, it was successfully applied to eight soybean genotypes harvested from two locations, and the resulting correlations of carbohydrate and oil or protein are presented. This methodology has the potential not only to guide soybean cultivar optimization processes but also to be expanded to other crops with only slight modifications. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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Article
GC-MS Phytochemical Profiling, Pharmacological Properties, and In Silico Studies of Chukrasia velutina Leaves: A Novel Source for Bioactive Agents
Molecules 2020, 25(15), 3536; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25153536 - 02 Aug 2020
Cited by 23 | Viewed by 2132
Abstract
Chukrasia velutina is a local medicinal plant commonly known as chikrassy in Bangladesh, India, China, and other South Asian countries. The leaves, bark, and seeds are vastly used as herbal medicine for fever and diarrhea, and its leaves essential oils are used for [...] Read more.
Chukrasia velutina is a local medicinal plant commonly known as chikrassy in Bangladesh, India, China, and other South Asian countries. The leaves, bark, and seeds are vastly used as herbal medicine for fever and diarrhea, and its leaves essential oils are used for antimicrobial purposes. In this study, we discuss the neuropsychiatric properties of C. velutina leaves through several animal models, quantitative and qualitative phytochemical analysis, and computational approaches. Neuropsychiatric effects were performed in rodents on the methanolic extract of C. velutina leaves (MECVL). Antidepressant, anxiolytic, and sedative effects experimented through these rodent models were used such as the force swimming test (FST), tail suspension test (TST), hole board test (HBT), elevated plus maze test (EPMT), light/dark box test (LDBT), open field test (OFT), and hole cross test (HCT). In these rodent models, 200 and 400 mg/kg doses were used which exhibited a significant result in the force swimming and tail suspension test (p < 0.001) for the antidepressant effect. In the anxiolytic study, the results were significant in the hole board, elevated plus maze, and light/dark box test (p < 0.001) for doses of 200 and 400 mg/kg. The result was also significant in the open field and hole cross test (p < 0.001) for sedative action in the sake of similar doses. Moreover, qualitative and quantitative studies were also performed through phytochemical screening and GC-MS analysis, and fifty-seven phytochemical compounds were found. These compounds were analyzed for pharmacokinetics properties using the SwissADME tool and from them, thirty-five compounds were considered for the molecular docking analysis. These phytoconstituents were docking against the human serotonin receptor, potassium channel receptor, and crystal structure of human beta-receptor, where eight of the compounds showed a good binding affinity towards the respective receptors considered to the reference standard drugs. After all of these analyses, it can be said that the secondary metabolite of C. velutina leaves (MECVL) could be a good source for inhibiting the neuropsychiatric disorders which were found on animal models as well as in computational studies. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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Article
Extraction of Lipids from Liquid Biological Samples for High-Throughput Lipidomics
Molecules 2020, 25(14), 3192; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25143192 - 13 Jul 2020
Cited by 2 | Viewed by 1147
Abstract
Extraction of the lipid fraction is a key part of acquiring lipidomics data. High-throughput lipidomics, the extraction of samples in 96w plates that are then run on 96 or 384w plates, has particular requirements that mean special development work is needed to fully [...] Read more.
Extraction of the lipid fraction is a key part of acquiring lipidomics data. High-throughput lipidomics, the extraction of samples in 96w plates that are then run on 96 or 384w plates, has particular requirements that mean special development work is needed to fully optimise an extraction method. Several methods have been published as suitable for it. Here, we test those methods using four liquid matrices: milk, human serum, homogenised mouse liver and homogenised mouse heart. In order to determine the difference in performance of the methods as objectively as possible, we used the number of lipid variables identified, the total signal strength and the coefficient of variance to quantify the performance of the methods. This showed that extraction methods with an aqueous component were generally better than those without for these matrices. However, methods without an aqueous fraction in the extraction were efficient for milk samples. Furthermore, a mixture containing a chlorinated solvent (dichloromethane) appears to be better than an ethereal solvent (tert-butyl methyl ether) for extracting lipids. This study suggests that a 3:1:0.005 mixture of dichloromethane, methanol and triethylammonium chloride, with an aqueous wash, is the most efficient of the currently reported methods for high-throughput lipid extraction and analysis. Further work is required to develop non-aqueous extraction methods that are both convenient and applicable to a broad range of sample types. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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Article
Simultaneously Quantitative Analysis of Naringin and Its Major Human Gut Microbial Metabolites Naringenin and 3-(4′-Hydroxyphenyl) Propanoic Acid via Stable Isotope Deuterium-Labeling Coupled with RRLC-MS/MS Method
Molecules 2019, 24(23), 4287; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24234287 - 25 Nov 2019
Cited by 6 | Viewed by 1424
Abstract
Widespread in citrus fruits, naringin, a natural 2,3-dihydroflavonoid, is of particular interest to scientists and has a broad range of beneficial bioactivities to health. Orally administered naringin remains in the gut tract for a relatively long time because of its low bioavailability. Under [...] Read more.
Widespread in citrus fruits, naringin, a natural 2,3-dihydroflavonoid, is of particular interest to scientists and has a broad range of beneficial bioactivities to health. Orally administered naringin remains in the gut tract for a relatively long time because of its low bioavailability. Under the metabolism mediated by human gut microbiota, naringin could be an active precursor for derived metabolites to play important physiological roles. However, naringin and its metabolites are hard to accurately quantify due to severe endogenic interference. In this study, an analytical rapid resolution liquid chromatography tandem mass spectrometry (RRLC-MS/MS) method coupled with stable isotope deuterium-labeling is developed and validated to simultaneously quantify naringin as well as its major human gut microbial metabolites naringenin and 3-(4′-hydroxyphenyl) propanoic acid. By eliminating the matrix interferences, this strategy not only confirms naringenin and 3-(4′-hydroxyphenyl) propanoic acid as the predominant metabolites which contribute to the pharmacological effects of naringin but also provides a suitable choice for other flavonoid pharmacokinetics study. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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Article
Volatiles from the Mandibular Gland Reservoir Content of Colobopsis explodens Laciny and Zettel, 2018, Worker Ants (Hymenoptera: Formicidae)
Molecules 2019, 24(19), 3468; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24193468 - 24 Sep 2019
Cited by 3 | Viewed by 1285
Abstract
Forty-five volatile organic compounds (VOCs) were identified or annotated in the mandibular gland reservoir content (MGRC) of the Southeast Asian ant Colobopsis explodens Laciny and Zettel, 2018 (Hymenoptera: Formicidae), using headspace solid-phase microextraction (HS-SPME) coupled to gas chromatography-mass spectrometry (GC-MS) and liquid extraction [...] Read more.
Forty-five volatile organic compounds (VOCs) were identified or annotated in the mandibular gland reservoir content (MGRC) of the Southeast Asian ant Colobopsis explodens Laciny and Zettel, 2018 (Hymenoptera: Formicidae), using headspace solid-phase microextraction (HS-SPME) coupled to gas chromatography-mass spectrometry (GC-MS) and liquid extraction combined with GC-MS. In extension of previous reports on VOCs of C. explodens, members of different compound classes, such as alkanes, aliphatic and aromatic carboxylic acids, and phenolics, were detected. The ketone 2-heptanone and the biochemically related phenolics benzene-1,3,5-triol (phloroglucinol, PG), 1-(2,4,6-trihydroxyphenyl)ethanone (monoacetylphloroglucinol, MAPG), 5,7-dihydroxy-2-methylchromen-4-one (noreugenin), and 1-(3-Acetyl-2,4,6-trihydroxyphenyl)ethanone (2,4-diacetylphloroglucinol, DAPG) dominated the GC-MS chromatograms. The identities of the main phenolics MAPG and noreugenin were further verified by liquid chromatography-high resolution-tandem mass spectrometry (LC-HRMS/MS). A comparative study of MGRC samples originating from three distinct field expeditions revealed differences in the VOC profiles, but the presence and relative abundances of the dominating constituents were largely consistent in all samples. Our study considerably extends the knowledge about the number and type of VOCs occurring in the MGRC of C. explodens. Based on the type of the detected compounds, we propose that the likely irritant and antibiotic phenolic constituents play a role in defense against arthropod opponents or in protection against microbial pathogens. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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Article
Taste Evaluation of Yellowtail (Seriola Quinqueradiata) Ordinary and Dark Muscle by Metabolic Profiling
Molecules 2019, 24(14), 2574; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24142574 - 15 Jul 2019
Cited by 4 | Viewed by 1404
Abstract
We performed metabolic profiling on yellowtail (Seriola quinqueradiata) muscle to develop an objective taste evaluation method for fish meat. Dark (DM) and ordinary (OM) muscle samples before and after storage were subjected to gas chromatography-mass spectrometry (GC-MS) analysis and taste measurements [...] Read more.
We performed metabolic profiling on yellowtail (Seriola quinqueradiata) muscle to develop an objective taste evaluation method for fish meat. Dark (DM) and ordinary (OM) muscle samples before and after storage were subjected to gas chromatography-mass spectrometry (GC-MS) analysis and taste measurements using an electronic tongue. The metabolites identified by the GC-MS analysis were treated as x variables, and the taste values obtained by the electronic tongue were treated as y variables. The relationships between the metabolites and taste attributes were evaluated by two-way orthogonal projections to latent structures (O2PLS) analysis. The O2PLS analyses were normalized in two ways, unit variance (UV) and pareto (Par) scaling. The O2PLS (UV) analysis produced 3+1+0 models in Autofit and this model was statistically significant with R2Y (0.73) and Q2 (0.52) metrics. In particular, significant correlations were found between DM or OM and metabolite intensity and taste attributes, and strong associations were found between “sourness” and lysine, “irritant” and alanine and phenylalanine, “saltiness” and pantothenic acid, and “umami” and creatinine and histidine. The O2PLS (Par) analysis of DM generated significant predictive models for “acidic bitterness,” “irritant,” “saltiness,” “bitterness,” “astringency,” and “richness.” Among these, only “irritant” was affected by storage. This method was thus effective in evaluating the taste of yellowtail muscle. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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Article
Hexagonal Mesoporous Silica as a Rapid, Efficient and Versatile Tool for MALDI-TOF MS Sample Preparation in Clinical Peptidomics Analysis: A Pilot Study
Molecules 2019, 24(12), 2311; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24122311 - 22 Jun 2019
Cited by 3 | Viewed by 2384
Abstract
Improvement in high-throughput MALDI-TOF MS analysis requires practical and efficient sample preparation protocols for high acquisition rates. The use of hexagonal mesoporous silica (HMS) sorbents in combination with MALDI-TOF MS was explored as a versatile tool for peptidomic profiling of clinical specimens difficult [...] Read more.
Improvement in high-throughput MALDI-TOF MS analysis requires practical and efficient sample preparation protocols for high acquisition rates. The use of hexagonal mesoporous silica (HMS) sorbents in combination with MALDI-TOF MS was explored as a versatile tool for peptidomic profiling of clinical specimens difficult to process, but considered important sources of disease biomarkers: synovial fluid and sputum. A rapid and efficient procedure, based on dispersive solid-phase extraction of peptides using commercially available wormhole mesostructured HMS, was tested for: a) pre-concentration of standard peptides in serially diluted solution up to the sub-nanomolar range; b) peptidome profiling of sputum and synovial fluid. The use of HMS, as dispersed sponges, significantly amplified the peptidic repertoire of sputum and synovial fluid by excluding from the adsorptive process large size proteins, which mask and/or suppress peptidome signals. The protocol proposed, as dispersive solid phase extraction, ensures good analytical performances. Moreover, it is economical and rapid, as it avoids the use of less reproducible and prolonged sample preparation procedures, such as the use of ultrafiltration filter devices. These findings may contribute to defining a high-throughput screening MS-based platform for monitoring key peptidic features of difficult to analyse bodily fluids in a clinical setting. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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Article
Metabolic Effect of Dietary Taurine Supplementation on Grouper (Epinephelus coioides): A 1H-NMR-Based Metabolomics Study
Molecules 2019, 24(12), 2253; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24122253 - 17 Jun 2019
Cited by 17 | Viewed by 1561
Abstract
Taurine is an indispensable amino acid for many fish species and taurine supplementation is needed when plant-based diets are used as the primary protein source for these species. However, there is limited information available to understand the physiological or metabolic effects of taurine [...] Read more.
Taurine is an indispensable amino acid for many fish species and taurine supplementation is needed when plant-based diets are used as the primary protein source for these species. However, there is limited information available to understand the physiological or metabolic effects of taurine on fish. In this study, 1H nuclear magnetic resonance (NMR)-based metabolomic analysis was conducted to identify the metabolic profile change in the fish intestine with the aim to assess the effect of dietary taurine supplementation on the physiological and metabolomic variation of fish, and reveal the possible mechanism of taurine’s metabolic effect. Grouper (Epinephelus coioides) were divided into four groups and fed diets containing 0.0%, 0.5%, 1.0%, and 1.5% taurine supplementation for 84 days. After extraction using aqueous and organic solvents, 25 significant taurine-induced metabolic changes were identified. These metabolic changes in grouper intestine were characterized by differences in carbohydrate, amino acid, lipid and nucleotide. The results reflected both the physiological state and growth of the fish, and indicated that taurine supplementation significantly affects the metabolome of fish, improves energy utilization and amino acid uptake, promotes protein, lipid and purine synthesis, and accelerates fish growth. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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Article
Effects of Silymarin on the In Vivo Pharmacokinetics of Simvastatin and Its Active Metabolite in Rats
Molecules 2019, 24(9), 1666; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules24091666 - 28 Apr 2019
Cited by 14 | Viewed by 1351
Abstract
Herein, the effect of silymarin pretreatment on the pharmacokinetics of simvastatin in rats was evaluated. To ensure the accuracy of the results, a rapid and sensitive UPLC–MS/MS method was established for simultaneous quantification of simvastatin (SV) and its active metabolite simvastatin acid (SVA). [...] Read more.
Herein, the effect of silymarin pretreatment on the pharmacokinetics of simvastatin in rats was evaluated. To ensure the accuracy of the results, a rapid and sensitive UPLC–MS/MS method was established for simultaneous quantification of simvastatin (SV) and its active metabolite simvastatin acid (SVA). This method was applied for studying the pharmacokinetic interactions in rats after oral co-administration of silymarin (45 mg/kg) and different concentrations of SV. The major pharmacokinetic parameters, including Cmax, tmax, t1/2, mean residence time (MRT), elimination rate constant (λz) and area under the concentration-time curve (AUC0–12h), were calculated using the non-compartmental model. The results showed that the co-administration of silymarin and SV significantly increased the Cmax and AUC0–12h of SVA compared with SV alone, while there was no significant difference with regards to Tmax and t1/2. However, SV pharmacokinetic parameters were not significantly affected by silymarin pretreatment. Therefore, these changes indicated that drug-drug interactions may occur after co-administration of silymarin and SV. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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Review

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Review
Emerging Techniques for Differentiation of Fresh and Frozen–Thawed Seafoods: Highlighting the Potential of Spectroscopic Techniques
Molecules 2020, 25(19), 4472; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25194472 - 29 Sep 2020
Cited by 13 | Viewed by 1548
Abstract
Fish and other seafood products have a limited shelf life due to favorable conditions for microbial growth and enzymatic alterations. Various preservation and/or processing methods have been developed for shelf-life extension and for maintaining the quality of such highly perishable products. Freezing and [...] Read more.
Fish and other seafood products have a limited shelf life due to favorable conditions for microbial growth and enzymatic alterations. Various preservation and/or processing methods have been developed for shelf-life extension and for maintaining the quality of such highly perishable products. Freezing and frozen storage are among the most commonly applied techniques for this purpose. However, frozen–thawed fish or meat are less preferred by consumers; thus, labeling thawed products as fresh is considered a fraudulent practice. To detect this kind of fraud, several techniques and approaches (e.g., enzymatic, histological) have been commonly employed. While these methods have proven successful, they are not without limitations. In recent years, different emerging methods have been investigated to be used in place of other traditional detection methods of thawed products. In this context, spectroscopic techniques have received considerable attention due to their potential as being rapid and non-destructive analytical tools. This review paper aims to summarize studies that investigated the potential of emerging techniques, particularly those based on spectroscopy in combination with chemometric tools, to detect frozen–thawed muscle foods. Full article
(This article belongs to the Special Issue Modern Analytical Techniques in Metabolomics Analysis)
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